Checking some Youtube videos about censorship in Yu-Gi-Oh! (especcially this video), it seems that the motives for censorship are based mainly on:
- Sexual content/innuendoes
- Violence
- Religion references
- And others (offensive language, stereotypes, political matters, etc.)
There is a entire list of modified cards, but I'm looking for Kazuki Takahashi's words about this subject that covers censorship in his anime, manga and cards1.
1 The linked sources shows the reasons for censorship (i.e changes made in scenes and artwork card modifcations), but none of them mentions Kazuki Takahashi's opinion.